Inquisitor Naruto
by Adeptus Terra
Summary: Warhammer 40K crossover. After the Kyuubi was sealed within Naruto mysteriously appeared on Holy Terra, in the hands of the Inquisition. He was raised as a member of the inquisition since birth, Naruto is now returning to his lost homeworld.
1. From Birth to Warp

Disclaimer: I own nothing here.

_Twelve Years ago_

Ordo Hereticus Citadel, Holy Terra

Inquisitor Scholar Xanthis Lok walked down the stone hallway of the citadel, heading toward a cell holding an infant that had fallen out of the warp not even an hour ago. Normally such a child would be killed immediately, for nothing can touch the warp without being tainted by Chaos, but a Sanctioned Psyker on the scene reported something strange, beyond the fact that the infant was a daemonhost, so here he was called in, though in all honesty Xanthis doubted that anything he could find would spare the infant its life.

Opening the iron door to the cell Xanthis saw two members of the Adepta Sororitas overlooking the daemonhost infant with a mixture of pity and absolute hate and disgust, and Xanthis could understand, someone thrust a daemon into a newborn infant, a vile and foul act only the servants of Chaos would do. Xanthis looked over at one of the Sisters before looking at the daemon seal on the child. He inspected the seal carefully before his eyes went wide with shock, what he was seeing was impossible, and certainly not an act of Chaos. Looking back at the Sisters of Battle, Inquisitor Scholar Xanthis spoke with a stern voice of command, "Watch the child and ensure nothing happens to him, I want him unharmed until I say otherwise." And with that he walked out of the cell.

Entering the office of The Ordo Hereticus High Inquisitor, Xanthis bowed with respect due to the High Inquisitor's station before speaking, "My Lord, the daemonhost infant, he should not be harmed. Whatever happened to him is not the work of the Great Enemy."

Before Inquisitor Xanthis could continue the High Inquisitor held up his hand to stop him and said, "You'd best have a good explanation, an infant could not withstand the pressure a daemon could put upon it, and the infant should be killed before he becomes possessed."

"That's just it milord, the daemon is quad bound, as long as the infant remains alive the daemon will weaken and in time, die forever. The seal placed upon the infant, a tattoo by the look of it, purifies the daemon's energies and feeds it into the infant. He has the possibility to become one of the most powerful Psyker of our generation. The seal is designed to hold at least a greater daemon. I would suggest we use a Psyker to scan the infant's mind and learn everything there is to learn about what happened to him and any clues to his identity and homeworld," Inquisitor Xanthis explained.

The High Inquisitor nodded and said, "The Ordo Malleus would be interested in any means to permanently destroy a daemon, and I agree, if what you say is true, he will be a powerful weapon against the forces of the Great Enemy. The infant will be your responsibility, and if he falls to Chaos, then you will share his fate, and to ensure that I will assign one of the Adepta Sororitas to watch over both the infant and you to ensure you don't fall to Chaos. Dismissed, and may the Emperor's light shine on your experiment."

Xanthis bow and said, "For the Emperor," before he turned on his heel and walked out of the High Inquisitor's office. When he returned to the infant's cell a Psyker was already standing over the infant scanning his mind. . The Psyker looked up after a couple of minutes and said in a raspy voice, "His name is Naruto Uzumaki, and he is from the village of Konoha, but other than that I have yet to gleam any useful information from his mind.

Xanthis nodded before picking up the infant and cradling the child in his arms as he looked down on the blonde haired infant's face and saying, "Hello Naruto, and welcome to the Inquisition."

_Today_

The Warp

The Warp twisted around the black ship of the Ordo Hereticus as it sailed through the chaos. On the bridge of the ship the Sanctioned Psyker of the Inquisition stood looking over a consol that gave a readout of the vile realm that made moving from world to world possible. He knew, even without his Psyker powers that his ghost was standing not that far from him, Sister Venus of the Adepta Sororitas, waiting for him to fall to the daemon he contained so that she could kill him. Somewhere else on the ship his adopted father, Inquisitor Xanthis, he was performing his duties.

"Emperor Preserve Us! Get us out of the Warp!" Naruto cried out as he saw something on the screen that made it feel like ice water had been poured through his veins, the screen showed a Warp storm was enveloping their ship. But it was too late, even as the black ship attempted to leave the Warp, the ship shook violently as a massive gash was torn in the ship. The people on the ship were flushed out into first the Warp, where they were immediately devoured by daemons, and then into the cold vacuum of space. As soon as the black ship reentered normal space, an abandon ship alarm rang throughout the ship.

Naruto and his ghost rushed toward the nearest way to get off the ship, drop pods, not exactly a smooth trip to the near by planet, but at least it would get them off of the dying ship. Naruto and Venus each hurried into a drop pod, and then the two drop pods launched out of the ship and down toward the planet, along with several others before the ship finally exploded, enveloping dozens of drop pods, shuttles, and escape pods.

Of the thousands of people once on the ship, only about a hundred survived the disaster and now sailed down toward the planet below, an uncharted planet, one that, though unknown to the people now falling to the world, was Naruto's homeworld. The Emperor's hand had guided Naruto home, though for what reasons was unknown at this time, in time everything will become clear.

Konoha

Kakashi was reading his newest _Icha Icha_ book when something caused his attention to look up, and when he did his uncovered eye went wide as flaming stars started to fall to the earth. He stood and put his book into his pouch as he stared at the flames that tore through the sky and he could feel in his soul that everything he thought he knew had changed forever. He was still staring at the burning sky when a massive explosion and a blast of rock and dust burst from the Hokage monument on the side of the mountain. One of the flaming stars that had fallen from heaven had struck the face of the First Hokage.

Kakashi immediately started to run and jump across the tops of near by buildings at his top speed toward the now damaged Hokage monument. And he would have reached there too, had another flaming star not slammed down into the building in front of him, forcing him to jump back to avoid being killed by the falling star.

Staring down into the wreckage of the building, Kakashi noted that it was a shop, and the lack of anyone injured or killed sent a feeling of relief, the shop had been closed and… Kakashi's train of though stopped as he looked at the object that had almost landed on top of him, it was a mix of pyramidal and cylindrical with what looked like three claws coming up above it. It was pure black except what looked like a large I with a skull on it and then another I carved into the skull's forehead.

With a hiss the walls of the strange object fell down, revealing the interior of the object, where a boy was standing, he was wearing flowing robes and holding an eagle headed staff, but the most astonishing thing to Kakashi was the fact that the boy held a striking resemblance to his old mentor, the fourth Hokage. Kakashi was looking at the boy, his hand ready to pull out a kunai at the first hostile move when the boy spoke, "I am Inquisitor Naruto Uzimaki, and in the name of the Emperor, you will tell me what world I have landed on."


	2. Planet Fall

Twelve Years ago

Konoha, Hokage's Tower

Kakashi and two ANBU Black Ops teams stood at the back of the Third Hokage's office as the boy who had identified himself as Inquisitor Naruto Uzimaki, and Kakashi recognized that name immediately, though he swore that his old Sensei's son had died with his mother and father with the Kyuubi attacked. At least that's what he had been told, and he never had any reason to doubt that, till now. And the man with Naruto was tall, bald and wearing black, red, and white robes that resembled the robes of a monk. He held a staff with a piece of paper at the top and a large book chained to his waste. What struck Kakashi as truly bizarre was that from under the man's robes were several metal tubes that went directly into the back of the man's head. When the man started to spoke Kakashi was broken out of his thoughts.

"…which is what brought us here; personally, I am Bishop Mercutio Wolfe, loyal servant of the Emperor, and member of the Adeptus Ministorum, though I currently work with the Inquisition. Inquisitor Uzimaki and I landed here in our drop pods. Which I have gathered has not yet even seen the light of the Emperor, or even moved beyond your own system," The man know known as Bishop Wolfe said, as Naruto stood silently next to him.

The Third Hokage took a puff of his pipe as he looked at Bishop Wolfe and Naruto, and as he mulled over what had just been said and he was also thinking back to those events of the attack, when that terrible, evil red tear had appeared and those horrific tentacles that had pulled the infant away from his crib. Between the events of that day, those strange pods that had crashed into the village, and the odd appearance of Bishop Wolfe, lead credence of his words.

Tipping his hat up the Third Hokage cleared his throat and said, "That's quite a claim, and given what I've seen I am inclined to believe you, but that's an unusual story you've told and I am forced to be suspicious of your story. While I think this over I will have you put up in a hotel, as well as have some public information given over to you so that you better understand our customs and situation. Kakashi, will you escort them."

Bishop Wolfe bowed slightly and said, "A suspicious mind is a healthy mind. And that would be acceptable, for now. I do hope that you would grant us a few buildings for both of us, and all the other survivors, as well as a place to establish a proper shrine to the God-Emperor of Mankind." With that said Kakashi led Bishop Wolfe and Naruto out of the Hokage's office.

After the two Imperials had left with Kakashi the third Hokage nodded to one of the ANBU teams and they immediately took off, tailing the Imperials. Once that they had left the Third said, "Cat, get me the council, I feel I will need their input on this situation." With that said the ANBU member wearing the Cat mask jumped out of the window and out of sight.

"That man's eyes were filled with contempt and hatred, and not just directed at us, but at everything that was his. And _Naruto_ could tell I was here, despite the stealth technique. Remember Sarutobi, that Hatred breeds war." A voice from the shadows said before it also disappeared.

Konoha, Streets

Bishop Wolfe and Inquisitor Uzimaki walked down the street looking at everything, when Naruto spoke in the High Gothic language spoken by the nobility of the Imperium, "We were being watched by a man cloaking himself in darkness and even now we are being tailed Lord Bishop."

Mercurio didn't even look at Naruto as he responded in the same Nobility based language, "Not surprising, these ninja are military, and since we landed in the center of their main base I would be more surprised if they weren't suspicious of us. These people need to be brought into the Imperium, but the two of us alone can not do it alone, we need to find the other survivors and we will need to sanctify a shrine to the Emperor as soon as possible to save these people's souls."

Naruto nodded and said, still in High Gothic, "This form of conquest reeks of Chaos, but in this circumstance I can understand it. We need to find other survivors, Inquisitor Lok's knowledge would be invaluable and one of the ship's Tech-Priests would be a gift of the Emperor right now. One of the Astropaths would the best option, then we could call a crusade upon this world, and bring it into the Imperium where it belongs."

Bishop Mecurio nodded and said, "I am certain that the Emperor will smile upon us for our work here. All of Man must join the Imperium and we will bring this world into the Imperium by any means, and I feel that Konoha will be our beachhead. Such is the divine will of the Emperor. Also know that I was briefed on you Inquisitor Uzimaki, and will not hesitate to terminate you if I feel you have fallen or are falling to Chaos."

Before Naruto could respond Kakashi interrupted them, speaking the basic human language since the Dark Age of Technology, saying, "This is the inn where the Hokage has arranged for you. While he decides what to do with your situation you are expected to not leave your room. I am certain that the info he has promised you will be arriving soon." Kakashi showed them to their room, and once they were inside he pulled out a pen and notebook and wrote down everything they said, even if they were speaking a language he couldn't understand. He knew that the code breaking division would go over it and see if they could figure out what they had been saying.

As Kakashi wrote down their conversation as he walked to the code breaker division of ANBU headquarters, Naruto and Bishop Mercurio were continueing there discussion, in essence plotting on the best manner to eventual take control of this world, and continued to discuss it for several hours when a knock on their door revealed a woman, she had black spiked hair, a brown overcoat, a black fishnet body stocking, and a brown miniskirt. With a flippant wave she said, "Hey, names Anko, I was told to give you these, and to answer any questions you have, so read, and I'll be staying next door if you need anything." With that said she tossed a bag to Naruto and walked off. When Naruto looked into the bag he saw a bundle of scrolls and several files and notebooks. All the information that had been promised no doubt censored and edited to show them in the best light while keeping military secrets hidden.

Bishop Mercurio smirked and said, "Well boy, I do think that we had best get to reading, we need to see what kind of heresy is breeding on this world."

_Several Hours Later _

Inside Naruto's Seal

The Kyuubi lay sleeping behind the bars of his cell when he heard a dark chuckling, something which caused him to open one of his eyes, and he couldn't see what was laughing, only three glowing eyes in the darkness beyond the bars of his cell. The eyes were pure white and stood in stark contrast to the utter black void which they were in. And the laugh, it sent a chill down his spine. It reminded him of the entity that had imprisoned him, but there was something else to it, this entity had a considerable Malice about it, and the Kyuubi could feel it.

"Ahh, the boy returns home to learn his fate at long last, to bring destruction to Chaos the likes of which has never been seen. Centuries of manipulating have finally started to pay off, and the great Four shall remember why **I **am a god to be feared." The entity in the darkness said in a gloating tone.

Kyuubi rose slightly at this, who was this being, and why was he telling him this. Kyuubi's head was off the ground and it was nearly pressing itself against the cage bars now, trying to see this being who radiated a sense of Malice that was unnerving, even to the Kyuubi himself. He then spoke, "What are you, and why are you telling me this?"

With another dark chuckle the entity said, "Because I wanted to, and I think that is all I will tell you for now. When the time is right I will allow you to awaken again." When he said that a wolf like six clawed hand waved out of the darkness and then the Kyuubi's world went black. The dark chuckle that came out of the entity as he left the seal caused Naruto to shift in his sleep, as he was suddenly wracked by horrific nightmares filled with complete and utter destruction, though come morning, he wouldn't remember any of it.

**AN: A couple of quick author comments **

**1) Thanks to all who reviewed, I do hope you enjoy it.**

**2) Dusel, it's not Yaoi, Naruto and Sasuke are not paired, but the main characters, just as they are in the Manga. They are foils and without Sasuke there to reflect Naruto, Naruto's story loses its weight. Also, he was raised within the Inquisition itself, and thus would enter its membership sooner than normal, so yes he is officially an Inquisitor. And he does have a shadow, her name is Sister Venus, a Sister of Battle introduced in the first chapter.**

**3) Xeno, while that is possible, I have not yet decided what the pairings will be, but I do try to keep an open mind about all possible pairings.**


	3. The Beginning of it all

**Several Days Later**

_Thousands of men stood in the desert, they were all identical, long trench coats that seemed to whip in the wind, and gas masks fitted tightly onto their faces. One could notice that number among these identical soldiers were several ninja as well. As one they raised their lasrifles, or swords in the case of the ninja, over their heads and cried out with a single voice, "For the Emperor."_

_There was a flash of white light and the massive forms of the Adeptus Arstates stood there staring down their adversaries under the pouring rain. The squad of seven marines was a good twenty feet from another group of seven pierced individuals. They stood in the alleyway of some city and it was silent, save for the hum of a power sword and a few plasma weapons, and there was also grinding as someone pulled the trigger on a chain sword. The Sergeant of the unit sneered at his pierced enemies and cried out, "For Russ and the Allfather!"_

_There was another flash, and now it was a bald man wearing green robes and sunken, empty eyes. Clawed hands seemingly reached outward, as if trying to grasp at something just out of reach and in the distance a hissing of serpents could almost be heard, yet, it was audible. Looking outward he seemed to be in a cell covered in runes and seals and he spoke in a horse, graveled voice, "Find me, Acolyte."_

And with that Naruto woke with a jump. He was breathing hard, but that did not distract him from noticing that the sun was already up or that Mercurio was standing at the window looking out. He seemed to be deep in thought when he said, "Hmmmm, finally you awaken."

"I would have awoken sooner, had the Emperor not blessed me with a two-fold vision"

Mercurio looked up from his work, he had been trying to repair a servo skull for days now, and turned to looked at Naruto for a moment and then said, "Yes, and what was this vision Psyker?"

A small, yet disturbing smile appeared on Naruto's face as she said in High Gothic, "Fist, that an Astropath is alive on this world, though something is keeping it from communicating offworld. Whatever this was did not however prevent him from contacting me through my dream. And most important, a vision of a glorious Crusade to bring this world into His light fought by the Guard and the Adeptus Astates, and some local ninja. Our mission here is blessed by his Divine hand, I am certain of it."

Mercurio smiled, the ivory inlay in his teeth clearly visible in the light of the early day as he slung a dark red leather jacket over his shoulders as the servo skull floated up and started to fly around the room. "If what you saw truly was a gift of the Emperor, then we must continue to use these Radical techniques boy, may he forgive us. Now hurry and get dressed our escort is waiting, we have much to do today after all."

Naruto nodded as he drew himself from his bed and looked over to his belongings. He didn't have much, even if the Hokage had provided some additional clothing and supplies to them. As Naruto slowly began to put on his own robes. They were a flowing brown coat that he had been wearing when he had landed in the village, and while not many would notice right away, it was far more than a normal jacket. He got it after aiding his father in destroying a Heretical Witch on Krieg. The truth of the jacket was that it was a piece of flak armor used by the legendary Death Korps, and offered him decent protection. It also looked like a robe when fully done up. He then checked his laspistol and extra ammo. Three clips he thought to himself, if he used the wisely and kept them solar charged they would last him for quite a long time.

Once he was fully dressed and prepared to go he turned back to Bishop Wolfe, who had drawn the hood of his coat up so that it covered the back of his skull. They had discovered that cerebral augmentation like Mercurio had was unheard of on this world, thus they did their best to spare the people the disquiet of having to witness it, at least for now. As Naruto took his staff he thought back to the last few days, and how apparently for the sake of "diplomacy" he was now to join the ninja academy. It was apparently his birthright as a member of the village, that had surprised both Naruto and Mercurio, the idea that this was Naruto's home world had raised a thousand questions, but none were asked, as it was not yet time.

Leaves of Fire Inn

Anko Mitarashi was bored, and while her room at the inn was nicer then her apartment, and room service paid for by the Hokage was definitely a plus, there was a limit to how much time she could do in a hotel room alone without being allowed to leave, something that was even restricted further by the order to remain alert and watch her charges. She had already racked up an impressive room service bill, and as long as she was here she had no intention of stopping.

Yawning Anko jumped out of the chair she had been lounging in and grabbed the heavy, thick book that Bishop had given her, he seemed to have a dozen of them. He said it contained many sermons on the Divinity of the Emperor and the most important tenants of the creed. She found the excepts on traitors particularly satisfying, given her own experiences with her mentor. She was reading one of the Sermons of a man named Sebastian Thor, she found it moving for reasons she couldn't quite explain when there was a knock on her door.

Standing Anko walked over to the door and opened it, already knowing who it was, the Imperials, as they were becoming known as. Once she opened the door she saw that her guess was right and with a half grin said, "Ok, I take it you want to go somewhere, so where to?"

Mercurio was stoic in Anko's opinion, no, that wasn't right, the man was cold. She chose to dress the way she did because it put people off guard and distracted them, even momentarily, but Wolfe had never even looked once, unlike the other one, Naruto. She also noticed the flying skull hovering about them with machinery weaved about it, and decided that it was fairly creepy. In response to her question Mercurio told her, "Last night your Hokage said a number of buildings would be turned over to us for use this morning. It's in a place called, the Uchiha Compound."

Though Anko didn't show it, she was far too well trained for that, the idea that the Uchiha compound had been given away to these strangers, that surprised her greatly. She could only guess that the Hokage was playing some long term gambit here, because otherwise he was going senile, which would be terrible, for everyone. She already knew that the boy Naruto would join the Academy, a month before graduation at that too, whatever the Hokage was planning was way over her pay grade, that was for certain. "Well then. Let's go before the Academy opens."

And with that the three of them left for the Uchiha compound, the Imperials were moving out, and while she wouldn't learn it until much later, she had also been reassigned to be their liaison, permanently. Clearly some of the council had decided that would be a fitting duty for a woman with questionable loyalties to begin with, Anko would simply be pissed.

The Kohana Ninja Academy

Naruto could feel the hate burning into his back from the boy sitting behind him, that Uchiha. he had not been there when he and Bishop Wolfe had arrived with their guide and claimed a building on the far side for their base of operations. The former base of the police if he remembered correctly, not that it mattered, the Uchiha compound no longer existed, it was now the Imperial Compound. Still, it was getting annoying. Turning the young psyker said, "And your problem is?"

"You stole my Home!" was the angry reply.

"No, I didn't, you still have your home. We only have the rest of the neighborhood, it's not like it was being used." Naruto said in a calm voice that only seemed to anger the Uchiha more. Several of the girls in the class seemed to be staring daggers at him as well for some reason.

"No, it was all my home!"

Before Naruto had a chance to reply the door opened and a ninja with a scar across his face appeared. That would be Iruka, Naruto surmised, his teacher, and even though the teacher didn't introduce himself he did mention that he would like to see Naruto after classes so he could gauge his skills. After pouring over some scrolls detailing something called a clone technique for a few hours target practice test began and the students made their way out onto the practice range.

"Alright, you know the drill for this test, five bulls eyes with no misses is the only way to pass. You can choose your own ranged weapon." Iruka said with a grin.

Naruto noticed that most of the other students pulled out those throwing daggers known as Kunai or shuriken, though one did produce a bow Naruto calmly drew his laspistol. Iruka gave his an odd look as the targeting implant in his right eye pinpointed the target. Five times the red light lashed out of the laspistol and burned a hole in the center of the target. Iruka, and most of the student's jaws dropped at the display.

From behind Naruto the Uchiha he had the small argument with earlier decided that it was time to get back at the thief who had stolen his home and threw a shuriken at Naruto. Once again he surprised everyone when he spun and held up his hand and the shuriken stopped dead, then dropped to the ground when Naruto closed his hand. "For those who don't know, I am Naruto Uzumaki, long lost son of this village, and I am an Imperial Psyker. That means this training is beneath me, and so are you." Naruto said proudly as he stared at Sasake.

He then turned and walked off, having passed his test and went back into the school where he met another teacher, a man named Mizuke. "Hey, your that new student aren't you, the imperial?"

Naruto stopped and looked at him for a moment before saying, "Yes.... why?"

"Well, I saw your little boast out in the yard, and you do know there's a faster way to graduate, right?"

"Really? And what way would that be?" Naruto said, with a little more than trace amount of eagerness in his voice.

"Well, let me tell you a secret, but don't tell anyone I told you...." Mizuke said with a small grin on his face.

**That Night**

Hokage's Tower

"We granted you hospitality, gave you considerable amount of land, granted you an incredible amount of latitude and the DAY that happened your ward STOLE a classified military scroll from this very building!" A council member screamed at Bishop Wolfe.

"And I had nothing to do with that, and I doubt he does either, until I have some proof. All I see is slander against us." Wolfe said with a calm voice. He was getting annoyed with these three fools and was seriously tempted to kill them all for wasting his time as they had been arguing for fifteen minutes now.

The argument was about to get far more heated when Naruto, the Hokage, and Iruka all walked up. In a calm voice the Hokage said, "Naruto didn't steal it, he was framed by Mizuke. Iruka here can verify that. Mizuke has been turned over to Ibiki for interrogation. This discussion is over."

The council members grumbled as they left, but they did with the Hokage and Iruka. Naruto and Mercurio then went inside their new home, which was next to the building that Mercurio was sanctifying as a chapel to the God Emperor. Speaking in High Gothic the Bishop asked, "So, how did the mission go?"

"Excellent, Bishop Wolfe, I have the contents of the scroll copied onto my data slate and can begin to learn and practice at my leisure. Iruka has also agreed to teach me the basics so I know how practice their techniques myself. Given what I saw tonight not only is this world, or at least this region of it unfamiliar with Psykers, these ninjas do employ powers beyond the scope of normal humans. I suspect some kind of mutation that allows an altered form of Psyker ability. but without a scholar we are limited...."

Naruto stopped his report when a loud noise came from the front door and both him and Wolfe turned and looked over to see Anko having kicked open the door with a large duffle bag on her shoulder. With an exceedingly unhappy look on her face she unleashed a torrent of profanities and then said, "By order of the Council, I am to live here with you. I suggest we all get used to it because it ain't changing.

**A/N: Sorry for the delay, RL problems, writers block, and other crap.**

**Holy Night: Byakugan would indeed be seen as a blessing while the Sharingan would not. As for the other clans, well wait and see.**

**Follower of Light: More than likely on survivors, though no Grey Knights, as it was a Black Ship of the Ordo Hereticus, and as such no space marines on it. Sisters of Battle on the other hand....**

**Uncle Joe: Technically you are right and to other members of the Inquisition, Naruto would not hold the rank of inquisitor. However from the outside they don't make such distinctions as it would subtract from the fear the Ordos create. A united front so to speak, thus he is an Inquisitor and at the same time, he is not.**


End file.
